After the decline of the Roman Empire, the further Christianization of Europe was to a large extent peaceful,[4] although Jews and Muslims were harshly prosecuted, to an extent of forced conversions in Byzantine empire. Encounters between Christians and Pagans were sometimes confrontational, and some Christian kings (Charlemagne, Olaf I of Norway) were known for their violence against pagans. The persecution of Christian heretics resumed in 1022, when fourteen people were burned at Orléans.[2] Around this time Bogomilism and Catharism appeared in Europe; these sects were seen as heretic by the Catholic Church, and the Inquisition was initially established to counter them. Heavily persecuted, these heresies were eradicated by the 14th century. The suppression of the Cathar (or "Albigensian") faith took the form of the Albigensian Crusade (1209–1229), a 20-year military campaign initiated by the Roman Catholic Church. Its violence was extreme even by medieval standards. Notable individuals who were executed for heresy in the late Middle Ages are Jerome of Prague, John Badby and Jan Hus. Only the Waldensians, another heretical Christian sect, managed to survive in remote areas in Northern Italy.

The Spanish and Portuguese Inquisition also went on to persecute Jews and Muslims. In Spain after the Reconquista, Jews were forced to either convert or be exiled. Many were killed. The persecution of Jews goes back to 12th-century Visigothic Spain after the emergence of the blood libel against Jews. Although the Spanish had agreed to allow Muslims the freedom of religion in 1492, this was often ignored. In 1501, Muslims were offered the choice of conversion or exile. In 1556, Arab or Muslim dress was forbidden, and in 1566 Arabic language as a whole was prohibited in Spain.[5] Jews were eventually expelled from England by King Edward I, too.

European Colonialism, that was accompanied by Christian evangelism and often by violence, led to the suppression of indigenous religions in the territories conquered or usurped by the Europeans. The Spanish colonization of the Americas largely destroyed the Aztec and Inca civilization. However, Colonialism (and later European Imperialism) as a whole were not motivated by religious zeal; the suppression of the indigenous religions was their side result, not their main purpose. Only partial aspects, like the Goa Inquisition, bear resemblance to the persecutions that occurred on the European continent. By the 18th century, persecutions of unsanctioned beliefs had been reduced in most Europeans countries to religious discrimination, in the form of legal restrictions on those who did not accept the official faith. This often included being barred from higher education, or from participation in the national legislature. In colonized nations, attempts to convert native peoples to Christianity became more encouraging and less forceful. In British India during the Victorian era, Christian converts were given preferential treatment for governmental appointments.

At the present time, most countries in which Christianity is the religion of the majority of the people, are either secular states or they embrace the separation of Church and State in another way. (A list of countries in which Christianity still is the state religion can be found at the article on State religion.) Some recent political conflicts are sometimes considered as religious persecution. Among these, there is the case of the Hue Vesak shootings in Vietnam on May 8, 1963 and the ethnic cleansing of Albanians, most of them Muslim, in Kosovo between 1992 to 1999, along with Bosnian Muslims.[7]

After he had adopted Christianity following the Battle of the Milvian Bridge, Constantine I issued the Edict of Milan in 313 (together with his co-emperor Licinius). Since 306 there had already had been several edicts that granted Christians religious toleration in parts of the Empire, but the Edict of Milan removed all obstacles to the Christian faith and made the Empire officially neutral with regard to religious worship. Constantine supported the church with his patronage; he had an extraordinary number of large basilicas built for the Christian church, and endowed it with land and other wealth.[8] In doing this, however, he required the Pagans "to foot the bill".[8] According to Christian chroniclers it appeared necessary to Constantine "to teach his subjects to give up their rites (...) and to accustom them to despise their temples and the images contained therein,"[9] which led to the closure of pagan temples due to a lack of support, their wealth flowing to the imperial treasure;[10] Constantine I did not need to use force to implement this;[8] his subjects are said to simply have obeyed him out of fear. Only the chronicler Theophanes has added that temples "were annihilated", but this is considered "not true" by contemporary historians.[11] According to the historian Ramsay MacMullen Constantine desired to obliterate non-Christians but lacking the means he had to be content with robbing their temples towards the end of his reign.[12] He resorted to derogatory and contemptuous comments relating to the old religion; writing of the "obstinacy" of the pagans, of their "misguided rites and ceremonial", and of their "temples of lying" contrasted with "the splendours of the home of truth".[13]

During the course of his life he progressively became more Christian and turned away from any syncretic tendencies he appeared to favour at times and thus demonstrating, according to his biographers, that "The God of the Christians was indeed a jealous God who tolerated no other gods beside him. The Church could never acknowledge that she stood on the same plane with other religious bodies, she conquered for herself one domain after another".[14]

After the 3-year-reign of Julian the Apostate (ruled 361 to 363), who revived the Roman state paganism for a short time, the later Christian Roman Emperors sanctioned "attacks on pagan worship".[15] Towards the end of the 4th century Theodosius worked to establish Catholicism as the privileged religion in the Roman Empire."Theodosius was not the man to sympathise with the balancing policy of the Edict of Milan. He set himself steadfastly to the work of establishing Catholicism as the privileged religion of the state, of repressing dissident Christians (heretics) and of enacting explicit legal measures to abolish Paganism in all its phases."[16]

Two hundred and fifty years after Constantine was converted and began the long campaign of official temple destruction and outlawing of non-Christian worship Justinian was still engaged in the war of dissent.[17]

The transformation that happened in the 4th century lies at the heart of the debate between those Christian authors who advocated religious persecution and those who rejected it.[15] Most of all, the advocates of persecution looked to the writings of Augustine of Hippo,[15] the most influential of the Christian Church Fathers in the Latin West.[18] Initially (in the 390s), he had been sceptical about the use of coercion in religious matters. However, he changed his mind after he had witnessed how the Donatists (a schismatic Christian sect) were "brought over to the Catholic unity by fear of imperial edicts." When Augustine had characterized himself in De utilitate credenti (392), he said he was cupidus veri, eager for truth.[19] But in his 93. letter he described himself as quietis avidus, needing rest, and gave as reason the agitating Donatist.[19] From a position that had trusted the power of philosophical argumentation, Augustine had moved to a position that emphasised the authority of the church.[19] Augustine had become convinced of the effectiveness of mild forms of persecution and developed a defence of their use. His authority on this question was undisputed for over a millennium in Western Christianity.[15] Within this Augustinian consensus there was only disagreement about the extent to which Christians should persecute heretics. Augustine advocated fines, imprisonment, banishment and moderate floggings, but, according to Henry Chadwick, "would have been horrified by the burning of heretics."[20] In late Antiquity those burnings appear very rare indeed, the only certain case being the execution of Priscillian and six of his followers in 385. This sentence was roundly condemned by bishops like Ambrose, Augustine's mentor.[21]

In contrast to the late antiquity, the execution of heretics was much more easily approved in the late Middle Ages, after the Christianization of Europe was largely completed. The first known case is the burning of fourteen people at Orléans in 1022.[21] In the following centuries groups like the Bogomils, Waldensians, Cathars and Lollards were persecuted throughout Europe. The Fourth Council of the Lateran (1215) codified the theory and practise of persecution.[21] In its third canon, the council declared: "Secular authorities, whatever office they may hold, shall be admonished and induced and if necessary compelled by ecclesiastical censure, .. to take an oath that they will strive .. to exterminate in the territories subject to their jurisdiction all heretics pointed out by the Church."[22]

Saint Thomas Aquinas summed up the standard medieval position, when he declared that that obstinate heretics deserved "not only to be separated from the Church, but also to be eliminated from the world by death"[23]

The Protestant Reformation changed the face of Western Christianity forever, but initially it did nothing to change the Christian endorsement of religious persecution. The Reformers "fully embraced" Augustine's advocacy of coercion in religious matters, and many regarded the death penalty for heresy as legitimate.[21] Furthermore, by presenting a much more powerful threat to Catholic unity than the heretic groups of the Middle Ages, the Reformation led to the intensification of persecution under Catholic regimes.

Martin Luther had written against persecution in the 1520s, and had demonstrated genuine sympathy towards the Jews in his earlier writings, especially in Das Jesus ein geborener Jude sei (That Jesus was born as a Jew) from 1523, but after 1525 his position hardened. In Wider die Sabbather an einen guten Freund (Against the Sabbather to a Good Friend), 1538, he still considered a conversion of the Jews to Christianity as possible,[25] but in 1543 he published On the Jews and their Lies, a "violent anti-semitic tract."[26]

John Calvin helped to secure the execution for heresy of Michael Servetus,[27] although he unsuccessfully requested that he should be beheaded instead of being burned at the stake.

Effectively, however, the 16th-century Protestant view was less extreme than the mediaeval Catholic position. In England, John Foxe, John Hales, Richard Perrinchief, Herbert Thorndike and Jonas Proast all only saw mild forms of persecution against the English Dissenters as legitimate.[28] But (with the probable exception of John Foxe), this was only a retraction in degree, not a full rejection of religious persecution. There is also the crucial distinction between dissent and heresy to consider. Most dissenters disagreed with the Anglican Church only on secondary matters of worship and ecclesiology, and although this was a considered a serious sin, only a few 17th-century Anglican writers thought that this 'crime' deserved the death penalty.[29]

While the Christian theologians mentioned above advocated religious persecution to various extents, it was also Christians who helped pioneer the concept of religious toleration.

In his book on 'The English Reformation', particularly in the chapter 'The Origins of Religious Toleration', the late A. G. Dickens argued that from the beginning of the Reformation there had "existed in Protestant thought – in Zwingli, Melanchthon and Bucer, as well as among the Anabaptists – a more liberal tradition, which John Frith was perhaps the first echo in England".[32] Condemned for heresy, Frith was burnt at the stake in 1533. In his own mind, he died not because of the denial of the doctrines on purgatory and transubstantiation but "for the principle that a particular doctrine on either point was not a necessary part of a Christian's faith".[33] In other words, there was an important distinction to be made between a genuine article of faith and other matters where a variety of very different conclusions should be tolerated within the Church. This stand against unreasonable and profligate dogmatism meant that Frith, "to a greater extent than any other of our early Protestants", upheld "a certain degree of religious freedom".[33]

Frith was not alone. John Foxe, for example, "strove hard to save Anabaptists from the fire, and he enunciated a sweeping doctrine of tolerance even towards Catholics, whose doctrines he detested with every fibre of his being".[34]

In the early 17th century, Thomas Helwys was principal formulator of that distinctively Baptist request: that the church and the state be kept separate in matters of law, so that individuals might have a freedom of religious conscience. Helwys said the King "is a mortal man, and not God, therefore he hath no power over the mortal soul of his subjects to make laws and ordinances for them and to set spiritual Lords over them".[35]King James I had Helwys thrown into Newgate prison, where he had died by 1616 at about the age of forty.

By the time of the English Revolution Helwys' stance on religious toleration was more commonplace. However, whilst accepting their zeal in desiring a 'godly society', some contemporary historians doubt whether the English Puritans during the English Revolution were as committed to religious liberty and pluralism as traditional histories have suggested. However, historian John Coffey's recent work[36] emphasises the contribution of a minority of radical Protestants who steadfastly sought toleration for heresy, blasphemy, Catholicism, non-Christian religions, and even atheism. This minority included the Seekers, as well as the General Baptists and the Levellers. Their collective witness demanded the church be an entirely voluntary, non-coercive community able to evangelise in a pluralistic society governed by a purely civil state. Such a demand was in sharp contrast to the ambitions of the magisterial Protestantism of the Calvinist majority.

All of these considered themselves Christians or were actual churchmen. John Milton and John Locke are the predecessors of modern liberalism. Although Milton was a Puritan and Locke an Anglican, Areopagitica and A Letter concerning Toleration are canonical liberal texts.[40] Only from the 1690s onwards the philosophy of Deism emerged, and with it a third group that advocated religious toleration, but, unlike the radical Protestants and the Anglicans, also rejected biblical authority; this group prominently includes Voltaire, Frederick II of Prussia, Joseph II, Holy Roman Emperor, Thomas Jefferson and the English-Irish philosopher John Toland.[38] When Toland published the writings of Milton, Edmund Ludlow and Algernon Sidney, he tried to downplay the Puritan divinity in these works.[41]

That the North American colonies and later the United States provided a refuge for religious minorities from Europe partly explains the higher degree of religiosity in the contemporary United States and the "unusual sectarian quality of U.S. Protestantism".[43] Compared to Europe, "the United States has a superabundance of denominations and sects (...) as well as a far higher ratio of churchgoers."[44] Which importance the Christian religion should have in the United States, with its strong concept of Separation of church and state, is a contentious question. For Kevin Phillips, who wrote a book with the polemical title American Theocracy, "few questions will be more important to the twenty-first-century United States than whether renascent religion and its accompanying hubris will be carried on the nation's books as an asset or as a liability."[45]

According to a 2008 survey, 65% of US-American Christians believe that many religions can lead to eternal life.[46] 52% of US-American Christians think that at least some non-Christian faiths can lead to eternal life.[46]

(At its surface, the percentages above seem contradictory; the key is in the appellation of the term non-Christian in the second, lesser quantity. For some Christians, different sects of Christianity represent "different religions." These people thus mistake the survey term "many religions" to mean "different sects of Christianity," even though that is not the common intended use of the phrase. What the survey really shows is that more US Christians believe that God can make himself known through multiple Christian sects, than believe that He can make Himself known even through other religions. It is worth noting that a majority of US Christians take the more inclusive stance.)

It had long been the policy of the Catholic Church to support toleration of competing religions under such a scheme, but to support legal restrictions on attempts to convert Catholics to those religions, under the motto that "error has no rights".[citation needed]

On the seventh of December 1965 The Catholic Church as part of the Vatican II council issued the decree "Dignitatis humanae" that dealt with the rights of the person and communities to social and civil liberty in religious matters. It states: "2. The Vatican Council declares that the human person has a right to religious freedom. Freedom of this kind means that all men should be immune from coercion on the part of individuals, social groups and every human power so that, within due limits, nobody is forced to act against his convictions in religious matters in private or public, alone or in associations with others. The Vatican Council further declares that the right of religious freedom is based on the very word of God and by reason itself. This right of the human person to religious freedom must be given such recognition in the constitutional order of society as will make it a civic right...but if it [the civil authority] presumes to control or restrict religious activity it must be said to have exceeded the limits of its power...Therefore, provided the just requirements of public order are not violated, these groups [i.e. religious communities] have a right to immunity so that they may organize their own lives according to their religious principles...From this it follows that it is wrong for a public authority to compel its citizens by force or fear or any other means to profess or repudiate any religion or to prevent anyone from joining or leaving a religious body. There is even more serious transgression of God's will and of the sacred rights of the individual person and the family of nations when force is applied to wipe out or repress religion either throughout the whole world or in a single region or in a particular community".[47]

On 12 March 2000 Pope John Paul II prayed for forgiveness because "Christians have often denied the Gospel; yielding to a mentality of power, they have violated the rights of ethnic groups and peoples, and shown contempt for their cultures and religious traditions" [48]

Cardinal Joseph Ratzinger (Pope Benedict XVI) wrote "The quality of exemplarity which the honest admission of past faults can exert on attitudes within the Church and civil society should also be noted, for it gives rise to a renewed obedience to the Truth and to respect for the dignity and the rights of others, most especially, of the very weak. In this sense, the numerous requests for forgiveness formulated by John Paul II constitute an example that draws attention to something good and stimulates the imitation of it, recalling individuals and groups of people to an honest and fruitful examination of conscience with a view to reconciliation"[49]